Objectives
The SEQ-Sea project aims to sequence, assemble, and annotate the genomes of a significant portion of France’s marine biodiversity—approximately 4,500 species. Leveraging advanced technologies, this ambitious programme will deliver high-quality genomes, contributing to the understanding and preservation of marine ecosystems.
A key challenge lies in sequencing microscopic specimens, as high-quality sequencing requires sufficient amounts of tissue with high DNA concentration. Current protocols still require a minimum threshold of biological material to be effective.
1. DNA Extraction
SEQ-Sea teams recover frozen samples and extract DNA (as well as RNA) from cell nuclei. Extraction protocols are tailored to each taxonomic group or optimized on a case-by-case basis. The extracted DNA is then prepared for sequencing by fragmenting it and modifying the ends of the DNA fragments.
2. Genome Sequencing
DNA samples are sequenced using long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). While these platforms provide powerful sequencing capabilities, they must be complemented by additional techniques—such as Hi-C, which reveals chromosomal architecture within the nucleus—to reconstruct full chromosomal sequences.
3. Genome Assembly
Genome assembly is a critical step where DNA fragments are computationally aligned and merged to reconstruct the complete genome of each species. The objective is to produce high-quality, chromosome-level genome assemblies. Each assembly undergoes manual curation to ensure the accurate reconstruction of every chromosome.
4. Genome annotation
Genome annotation involves identifying genes and predicting their functions within the assembled genomes. This step is essential for understanding the biological roles of genes in marine organisms. The resulting gene catalog will be a valuable resource for the discovery of novel bioactive molecules.
Resources
The SEQ-Sea project is supported by the Genoscope’s state-of-the-art infrastructure, which enables the processing and analysis of large-scale genomic datasets. This includes high-throughput sequencers, data storage systems, and powerful computing resources—all of which are critical to the project’s success.
Organisation
Lead organisation : Genoscope (CEA), France Génomique
Manager : Jean-Marc AURY
Project managers : Caroline BELSER-MENGUY & Janaina RIGONATO